Starting phenix.real_space_refine on Tue Feb 13 09:09:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/02_2024/7kue_23036_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/02_2024/7kue_23036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/02_2024/7kue_23036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/02_2024/7kue_23036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/02_2024/7kue_23036_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/02_2024/7kue_23036_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 96 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 3 5.49 5 S 24 5.16 5 C 3049 2.51 5 N 780 2.21 5 O 866 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 264": "NH1" <-> "NH2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4726 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 499 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2342 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1854 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.39, per 1000 atoms: 0.72 Number of scatterers: 4726 At special positions: 0 Unit cell: (76.36, 83.83, 89.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 24 16.00 P 3 15.00 Al 1 13.00 F 3 9.00 O 866 8.00 N 780 7.00 C 3049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 723.8 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 1 sheets defined 42.1% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.577A pdb=" N ALA C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 298 through 310 removed outlier: 3.657A pdb=" N THR C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 55 removed outlier: 4.509A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 105 through 122 removed outlier: 4.321A pdb=" N TRP A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 184 through 200 removed outlier: 3.965A pdb=" N ASP A 187 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 188 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 190 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 200 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 263 through 270 Processing helix chain 'B' and resid 53 through 56 No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 62 through 74 Processing helix chain 'B' and resid 112 through 130 Processing helix chain 'B' and resid 135 through 151 removed outlier: 4.109A pdb=" N GLU B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 removed outlier: 3.809A pdb=" N VAL B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N HIS B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 224 through 228 removed outlier: 3.594A pdb=" N VAL B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 228' Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.685A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 286 removed outlier: 3.932A pdb=" N THR B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 343 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.883A pdb=" N VAL A 20 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 37 " --> pdb=" O VAL A 20 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 117 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 764 1.31 - 1.44: 1302 1.44 - 1.56: 2719 1.56 - 1.69: 10 1.69 - 1.81: 43 Bond restraints: 4838 Sorted by residual: bond pdb=" C1' ADP A 401 " pdb=" C2' ADP A 401 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1' ADP A 401 " pdb=" O4' ADP A 401 " ideal model delta sigma weight residual 1.426 1.628 -0.202 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" N ASN B 175 " pdb=" CA ASN B 175 " ideal model delta sigma weight residual 1.462 1.373 0.089 1.46e-02 4.69e+03 3.70e+01 bond pdb=" C5 ADP A 401 " pdb=" C6 ADP A 401 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 4833 not shown) Histogram of bond angle deviations from ideal: 78.50 - 91.42: 5 91.42 - 104.34: 89 104.34 - 117.26: 3281 117.26 - 130.18: 3145 130.18 - 143.10: 33 Bond angle restraints: 6553 Sorted by residual: angle pdb=" N ASP A 228 " pdb=" CA ASP A 228 " pdb=" C ASP A 228 " ideal model delta sigma weight residual 112.04 143.10 -31.06 1.44e+00 4.82e-01 4.65e+02 angle pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" C PHE B 177 " ideal model delta sigma weight residual 111.92 128.85 -16.93 1.34e+00 5.57e-01 1.60e+02 angle pdb=" C ASP A 228 " pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " ideal model delta sigma weight residual 110.56 88.28 22.28 1.83e+00 2.99e-01 1.48e+02 angle pdb=" O2P TPO A 162 " pdb=" P TPO A 162 " pdb=" O3P TPO A 162 " ideal model delta sigma weight residual 113.68 78.50 35.18 3.00e+00 1.11e-01 1.38e+02 angle pdb=" O1P TPO A 162 " pdb=" P TPO A 162 " pdb=" O3P TPO A 162 " ideal model delta sigma weight residual 115.11 80.11 35.00 3.00e+00 1.11e-01 1.36e+02 ... (remaining 6548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 2830 32.62 - 65.24: 77 65.24 - 97.86: 4 97.86 - 130.47: 0 130.47 - 163.09: 1 Dihedral angle restraints: 2912 sinusoidal: 1200 harmonic: 1712 Sorted by residual: dihedral pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual 122.80 167.36 -44.56 0 2.50e+00 1.60e-01 3.18e+02 dihedral pdb=" C PHE B 177 " pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual -122.60 -166.19 43.59 0 2.50e+00 1.60e-01 3.04e+02 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 136.91 163.09 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 2909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.402: 724 0.402 - 0.805: 4 0.805 - 1.207: 0 1.207 - 1.609: 0 1.609 - 2.012: 1 Chirality restraints: 729 Sorted by residual: chirality pdb=" CA PHE B 177 " pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CB PHE B 177 " both_signs ideal model delta sigma weight residual False 2.51 0.50 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA ASP A 228 " pdb=" N ASP A 228 " pdb=" C ASP A 228 " pdb=" CB ASP A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CB ILE A 72 " pdb=" CA ILE A 72 " pdb=" CG1 ILE A 72 " pdb=" CG2 ILE A 72 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.67e+00 ... (remaining 726 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 58 " -0.039 2.00e-02 2.50e+03 4.07e-02 4.15e+01 pdb=" CG TRP B 58 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP B 58 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP B 58 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 58 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 58 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 58 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 58 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 58 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 223 " -0.019 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C THR A 223 " 0.069 2.00e-02 2.50e+03 pdb=" O THR A 223 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO A 224 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 102 " 0.063 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO A 103 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.053 5.00e-02 4.00e+02 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 418 2.74 - 3.28: 4377 3.28 - 3.82: 7767 3.82 - 4.36: 8987 4.36 - 4.90: 15076 Nonbonded interactions: 36625 Sorted by model distance: nonbonded pdb=" CG PRO A 224 " pdb=" SD MET A 273 " model vdw 2.205 3.800 nonbonded pdb=" O SER A 287 " pdb=" OG SER A 287 " model vdw 2.328 2.440 nonbonded pdb=" OG1 THR A 88 " pdb=" O LEU A 135 " model vdw 2.342 2.440 nonbonded pdb=" OG SER B 153 " pdb=" OE1 GLN B 156 " model vdw 2.358 2.440 nonbonded pdb=" OD2 ASP B 224 " pdb=" OH TYR B 282 " model vdw 2.358 2.440 ... (remaining 36620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.77 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 2.500 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.080 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.222 4838 Z= 0.611 Angle : 1.620 35.182 6553 Z= 0.815 Chirality : 0.110 2.012 729 Planarity : 0.010 0.095 821 Dihedral : 15.459 163.093 1798 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.78 % Allowed : 1.36 % Favored : 97.87 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.28), residues: 560 helix: -3.26 (0.22), residues: 258 sheet: -3.17 (0.78), residues: 35 loop : -2.66 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.006 TRP B 58 HIS 0.008 0.001 HIS A 121 PHE 0.027 0.003 PHE B 177 TYR 0.055 0.003 TYR A 57 ARG 0.013 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8250 (mm) cc_final: 0.8025 (mm) REVERT: A 49 MET cc_start: 0.7567 (tpt) cc_final: 0.7328 (tpt) REVERT: A 62 GLN cc_start: 0.6934 (mp10) cc_final: 0.6594 (mp10) REVERT: A 91 GLU cc_start: 0.7155 (pp20) cc_final: 0.6933 (pp20) REVERT: A 131 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6998 (mtmt) REVERT: A 154 ILE cc_start: 0.7867 (mt) cc_final: 0.7608 (mt) REVERT: A 184 SER cc_start: 0.8464 (t) cc_final: 0.8216 (t) REVERT: A 272 THR cc_start: 0.8194 (p) cc_final: 0.7827 (p) REVERT: B 50 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7515 (mpp-170) REVERT: B 186 LYS cc_start: 0.7224 (ttmm) cc_final: 0.6990 (ttmm) REVERT: B 246 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7946 (ttmm) REVERT: B 270 THR cc_start: 0.7898 (p) cc_final: 0.7683 (p) outliers start: 4 outliers final: 3 residues processed: 145 average time/residue: 0.1988 time to fit residues: 35.3352 Evaluate side-chains 137 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 179 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 132 ASN B 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4838 Z= 0.258 Angle : 0.717 9.399 6553 Z= 0.367 Chirality : 0.050 0.339 729 Planarity : 0.007 0.073 821 Dihedral : 9.818 166.342 643 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.13 % Allowed : 10.47 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.32), residues: 560 helix: -2.07 (0.28), residues: 264 sheet: -2.95 (0.82), residues: 34 loop : -2.43 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP B 58 HIS 0.004 0.001 HIS A 121 PHE 0.015 0.002 PHE B 177 TYR 0.020 0.002 TYR B 237 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8277 (mm) cc_final: 0.8034 (mm) REVERT: A 49 MET cc_start: 0.7546 (tpt) cc_final: 0.7290 (tpt) REVERT: A 57 TYR cc_start: 0.7824 (m-80) cc_final: 0.7380 (m-80) REVERT: A 62 GLN cc_start: 0.7190 (mp10) cc_final: 0.6857 (mp10) REVERT: A 91 GLU cc_start: 0.7287 (pp20) cc_final: 0.7046 (pp20) REVERT: A 154 ILE cc_start: 0.8051 (mt) cc_final: 0.7807 (mt) REVERT: A 233 SER cc_start: 0.7704 (p) cc_final: 0.7265 (m) REVERT: A 236 MET cc_start: 0.5692 (tmm) cc_final: 0.5184 (tmm) REVERT: A 272 THR cc_start: 0.8509 (p) cc_final: 0.8133 (p) REVERT: B 50 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7547 (mpp-170) REVERT: B 223 LEU cc_start: 0.8159 (mt) cc_final: 0.7957 (mt) REVERT: B 246 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7929 (ttmm) outliers start: 11 outliers final: 7 residues processed: 149 average time/residue: 0.1932 time to fit residues: 35.2555 Evaluate side-chains 144 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4838 Z= 0.326 Angle : 0.738 7.924 6553 Z= 0.380 Chirality : 0.051 0.251 729 Planarity : 0.007 0.086 821 Dihedral : 9.414 159.181 640 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.49 % Allowed : 14.34 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.33), residues: 560 helix: -1.66 (0.29), residues: 268 sheet: -2.79 (1.02), residues: 22 loop : -2.53 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP B 58 HIS 0.009 0.002 HIS A 121 PHE 0.019 0.002 PHE A 266 TYR 0.019 0.002 TYR B 237 ARG 0.006 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8071 (pptt) cc_final: 0.7747 (pptt) REVERT: A 38 ILE cc_start: 0.8202 (mm) cc_final: 0.7975 (mm) REVERT: A 49 MET cc_start: 0.7433 (tpt) cc_final: 0.7187 (tpt) REVERT: A 62 GLN cc_start: 0.7279 (mp10) cc_final: 0.6944 (mp10) REVERT: A 91 GLU cc_start: 0.7478 (pp20) cc_final: 0.7128 (pp20) REVERT: A 154 ILE cc_start: 0.8155 (mt) cc_final: 0.7912 (mt) REVERT: A 233 SER cc_start: 0.8131 (p) cc_final: 0.7709 (m) REVERT: A 236 MET cc_start: 0.5665 (tmm) cc_final: 0.5375 (tmm) REVERT: A 272 THR cc_start: 0.8597 (p) cc_final: 0.8218 (p) REVERT: B 50 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7660 (mpp-170) REVERT: B 155 MET cc_start: 0.7281 (mtm) cc_final: 0.7063 (mtm) REVERT: B 186 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7434 (ttmm) REVERT: B 246 LYS cc_start: 0.8304 (ttmm) cc_final: 0.8005 (ttmm) outliers start: 18 outliers final: 12 residues processed: 159 average time/residue: 0.1919 time to fit residues: 37.3719 Evaluate side-chains 155 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4838 Z= 0.240 Angle : 0.678 7.418 6553 Z= 0.343 Chirality : 0.048 0.184 729 Planarity : 0.006 0.072 821 Dihedral : 8.898 149.369 640 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.26 % Allowed : 18.60 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.33), residues: 560 helix: -1.33 (0.30), residues: 267 sheet: -3.27 (0.87), residues: 27 loop : -2.53 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP B 58 HIS 0.008 0.001 HIS A 127 PHE 0.022 0.001 PHE A 266 TYR 0.016 0.001 TYR B 237 ARG 0.006 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8069 (pptt) cc_final: 0.7731 (pptt) REVERT: A 38 ILE cc_start: 0.8234 (mm) cc_final: 0.7978 (mm) REVERT: A 49 MET cc_start: 0.7469 (tpt) cc_final: 0.7234 (tpt) REVERT: A 57 TYR cc_start: 0.7847 (m-80) cc_final: 0.7568 (m-80) REVERT: A 62 GLN cc_start: 0.7299 (mp10) cc_final: 0.6994 (mp10) REVERT: A 91 GLU cc_start: 0.7496 (pp20) cc_final: 0.7144 (pp20) REVERT: A 154 ILE cc_start: 0.8157 (mt) cc_final: 0.7916 (mt) REVERT: A 233 SER cc_start: 0.8155 (p) cc_final: 0.7718 (m) REVERT: A 272 THR cc_start: 0.8565 (p) cc_final: 0.8136 (p) REVERT: B 50 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7522 (mpp-170) REVERT: B 246 LYS cc_start: 0.8307 (ttmm) cc_final: 0.7961 (ttmm) outliers start: 22 outliers final: 14 residues processed: 145 average time/residue: 0.2043 time to fit residues: 36.0211 Evaluate side-chains 146 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN B 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4838 Z= 0.330 Angle : 0.742 7.785 6553 Z= 0.377 Chirality : 0.052 0.194 729 Planarity : 0.007 0.073 821 Dihedral : 8.473 134.714 640 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.84 % Allowed : 18.60 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.34), residues: 560 helix: -1.20 (0.30), residues: 268 sheet: -3.25 (0.88), residues: 27 loop : -2.46 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP B 58 HIS 0.006 0.002 HIS A 127 PHE 0.023 0.002 PHE A 266 TYR 0.016 0.001 TYR B 60 ARG 0.008 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6854 (tt0) REVERT: A 12 LYS cc_start: 0.8135 (pptt) cc_final: 0.7799 (pptt) REVERT: A 38 ILE cc_start: 0.8242 (mm) cc_final: 0.7953 (mm) REVERT: A 49 MET cc_start: 0.7439 (tpt) cc_final: 0.7198 (tpt) REVERT: A 57 TYR cc_start: 0.7897 (m-80) cc_final: 0.7673 (m-80) REVERT: A 62 GLN cc_start: 0.7346 (mp10) cc_final: 0.7012 (mp10) REVERT: A 154 ILE cc_start: 0.8185 (mt) cc_final: 0.7937 (mt) REVERT: A 170 TYR cc_start: 0.7895 (m-80) cc_final: 0.7482 (m-80) REVERT: A 181 HIS cc_start: 0.7466 (p-80) cc_final: 0.7176 (p-80) REVERT: A 233 SER cc_start: 0.8374 (p) cc_final: 0.7990 (m) REVERT: B 50 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7562 (mpp-170) REVERT: B 246 LYS cc_start: 0.8329 (ttmm) cc_final: 0.7968 (ttmm) outliers start: 25 outliers final: 17 residues processed: 163 average time/residue: 0.2027 time to fit residues: 40.1921 Evaluate side-chains 161 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.0370 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4838 Z= 0.223 Angle : 0.674 6.824 6553 Z= 0.339 Chirality : 0.048 0.192 729 Planarity : 0.006 0.071 821 Dihedral : 7.875 122.787 640 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 5.43 % Allowed : 20.54 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.35), residues: 560 helix: -0.85 (0.32), residues: 259 sheet: -3.24 (0.89), residues: 27 loop : -2.33 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 58 HIS 0.007 0.001 HIS A 127 PHE 0.037 0.001 PHE A 266 TYR 0.014 0.001 TYR B 60 ARG 0.005 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6778 (tt0) REVERT: A 12 LYS cc_start: 0.8119 (pptt) cc_final: 0.7803 (pptt) REVERT: A 38 ILE cc_start: 0.8238 (mm) cc_final: 0.8030 (mm) REVERT: A 49 MET cc_start: 0.7469 (tpt) cc_final: 0.7224 (tpt) REVERT: A 57 TYR cc_start: 0.7803 (m-80) cc_final: 0.7513 (m-80) REVERT: A 62 GLN cc_start: 0.7370 (mp10) cc_final: 0.7012 (mp10) REVERT: A 76 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.7007 (p90) REVERT: A 150 LEU cc_start: 0.8294 (mp) cc_final: 0.8064 (mt) REVERT: A 154 ILE cc_start: 0.8129 (mt) cc_final: 0.7907 (mt) REVERT: A 181 HIS cc_start: 0.7466 (p-80) cc_final: 0.7194 (p-80) REVERT: A 233 SER cc_start: 0.8399 (p) cc_final: 0.7985 (m) REVERT: A 270 MET cc_start: 0.6909 (mtm) cc_final: 0.6649 (mtm) REVERT: B 50 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7556 (mpp-170) REVERT: B 114 LEU cc_start: 0.8043 (pp) cc_final: 0.7830 (mt) REVERT: B 196 LYS cc_start: 0.7458 (ptpp) cc_final: 0.6975 (ptpp) REVERT: B 216 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7803 (mttt) REVERT: B 246 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7936 (ttmm) outliers start: 28 outliers final: 17 residues processed: 155 average time/residue: 0.2057 time to fit residues: 38.6805 Evaluate side-chains 161 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4838 Z= 0.260 Angle : 0.702 10.330 6553 Z= 0.350 Chirality : 0.050 0.196 729 Planarity : 0.006 0.070 821 Dihedral : 7.530 110.061 640 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.04 % Allowed : 21.32 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.35), residues: 560 helix: -0.92 (0.31), residues: 260 sheet: -3.50 (1.03), residues: 17 loop : -2.22 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 229 HIS 0.006 0.001 HIS A 127 PHE 0.037 0.001 PHE A 266 TYR 0.013 0.001 TYR B 60 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 291 PHE cc_start: 0.7598 (m-80) cc_final: 0.6977 (m-80) REVERT: A 6 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6793 (tt0) REVERT: A 12 LYS cc_start: 0.8152 (pptt) cc_final: 0.7830 (pptt) REVERT: A 38 ILE cc_start: 0.8248 (mm) cc_final: 0.8029 (mm) REVERT: A 49 MET cc_start: 0.7469 (tpt) cc_final: 0.7249 (tpt) REVERT: A 57 TYR cc_start: 0.7846 (m-80) cc_final: 0.7578 (m-80) REVERT: A 62 GLN cc_start: 0.7381 (mp10) cc_final: 0.6983 (mp10) REVERT: A 76 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6901 (p90) REVERT: A 150 LEU cc_start: 0.8306 (mp) cc_final: 0.8104 (mt) REVERT: A 154 ILE cc_start: 0.8143 (mt) cc_final: 0.7917 (mt) REVERT: A 170 TYR cc_start: 0.7769 (m-80) cc_final: 0.7440 (m-80) REVERT: A 181 HIS cc_start: 0.7442 (p-80) cc_final: 0.7192 (p-80) REVERT: A 233 SER cc_start: 0.8427 (p) cc_final: 0.8016 (m) REVERT: A 270 MET cc_start: 0.6932 (mtm) cc_final: 0.6660 (mtm) REVERT: B 50 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7574 (mpp-170) REVERT: B 114 LEU cc_start: 0.8038 (pp) cc_final: 0.7797 (mt) REVERT: B 162 ILE cc_start: 0.8624 (mt) cc_final: 0.8412 (mm) REVERT: B 216 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7724 (mtpt) REVERT: B 246 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7953 (ttmm) outliers start: 26 outliers final: 21 residues processed: 163 average time/residue: 0.2000 time to fit residues: 39.4978 Evaluate side-chains 177 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.0670 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.4726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4838 Z= 0.200 Angle : 0.675 9.145 6553 Z= 0.332 Chirality : 0.047 0.203 729 Planarity : 0.006 0.070 821 Dihedral : 7.122 99.115 640 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.65 % Allowed : 21.90 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.35), residues: 560 helix: -0.73 (0.32), residues: 256 sheet: -3.34 (1.06), residues: 17 loop : -2.21 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 58 HIS 0.006 0.001 HIS A 127 PHE 0.032 0.001 PHE A 266 TYR 0.017 0.001 TYR B 60 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 291 PHE cc_start: 0.7575 (m-80) cc_final: 0.6895 (m-80) REVERT: A 6 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6784 (tt0) REVERT: A 12 LYS cc_start: 0.8187 (pptt) cc_final: 0.7888 (pptt) REVERT: A 38 ILE cc_start: 0.8240 (mm) cc_final: 0.8035 (mm) REVERT: A 49 MET cc_start: 0.7484 (tpt) cc_final: 0.7237 (tpt) REVERT: A 57 TYR cc_start: 0.7785 (m-80) cc_final: 0.7494 (m-80) REVERT: A 62 GLN cc_start: 0.7370 (mp10) cc_final: 0.6967 (mp10) REVERT: A 76 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6875 (p90) REVERT: A 110 MET cc_start: 0.7519 (tpp) cc_final: 0.7289 (mmm) REVERT: A 150 LEU cc_start: 0.8274 (mp) cc_final: 0.8071 (mt) REVERT: A 154 ILE cc_start: 0.8108 (mt) cc_final: 0.7892 (mt) REVERT: A 181 HIS cc_start: 0.7369 (p-80) cc_final: 0.7128 (p-80) REVERT: A 233 SER cc_start: 0.8368 (p) cc_final: 0.7961 (m) REVERT: B 50 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7571 (mpp-170) REVERT: B 65 LEU cc_start: 0.8323 (tp) cc_final: 0.8017 (tt) REVERT: B 114 LEU cc_start: 0.8048 (pp) cc_final: 0.7820 (mt) REVERT: B 216 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7703 (mtpt) REVERT: B 246 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7909 (ttmm) outliers start: 24 outliers final: 19 residues processed: 167 average time/residue: 0.1920 time to fit residues: 39.0209 Evaluate side-chains 173 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.0270 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4838 Z= 0.194 Angle : 0.689 8.478 6553 Z= 0.336 Chirality : 0.049 0.251 729 Planarity : 0.006 0.069 821 Dihedral : 6.936 91.141 640 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.46 % Allowed : 23.26 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.35), residues: 560 helix: -0.55 (0.33), residues: 251 sheet: -3.33 (1.08), residues: 17 loop : -2.25 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 58 HIS 0.006 0.001 HIS A 127 PHE 0.020 0.001 PHE B 119 TYR 0.018 0.001 TYR B 55 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 291 PHE cc_start: 0.7582 (m-80) cc_final: 0.6894 (m-80) REVERT: A 6 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6773 (tt0) REVERT: A 38 ILE cc_start: 0.8207 (mm) cc_final: 0.7995 (mm) REVERT: A 49 MET cc_start: 0.7501 (tpt) cc_final: 0.7244 (tpt) REVERT: A 57 TYR cc_start: 0.7768 (m-80) cc_final: 0.7473 (m-80) REVERT: A 62 GLN cc_start: 0.7376 (mp10) cc_final: 0.6969 (mp10) REVERT: A 76 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6881 (p90) REVERT: A 150 LEU cc_start: 0.8260 (mp) cc_final: 0.8050 (mt) REVERT: A 154 ILE cc_start: 0.8103 (mt) cc_final: 0.7870 (mt) REVERT: A 181 HIS cc_start: 0.7364 (p-80) cc_final: 0.7155 (p-80) REVERT: A 233 SER cc_start: 0.8365 (p) cc_final: 0.7941 (m) REVERT: B 50 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7594 (mpp-170) REVERT: B 114 LEU cc_start: 0.8056 (pp) cc_final: 0.7838 (mt) REVERT: B 167 ILE cc_start: 0.8271 (mt) cc_final: 0.7976 (mt) REVERT: B 216 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7695 (mtpt) REVERT: B 246 LYS cc_start: 0.8245 (ttmm) cc_final: 0.7879 (ttmm) outliers start: 23 outliers final: 19 residues processed: 162 average time/residue: 0.2125 time to fit residues: 41.9815 Evaluate side-chains 173 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 58 TRP Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 0.0040 chunk 12 optimal weight: 1.9990 overall best weight: 0.3490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4838 Z= 0.188 Angle : 0.693 8.124 6553 Z= 0.340 Chirality : 0.048 0.205 729 Planarity : 0.006 0.069 821 Dihedral : 6.759 84.057 640 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.26 % Allowed : 24.03 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.35), residues: 560 helix: -0.66 (0.32), residues: 257 sheet: -3.27 (1.10), residues: 17 loop : -2.20 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 58 HIS 0.005 0.001 HIS A 127 PHE 0.019 0.001 PHE B 148 TYR 0.017 0.001 TYR B 60 ARG 0.006 0.000 ARG A 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 291 PHE cc_start: 0.7570 (m-80) cc_final: 0.6871 (m-80) REVERT: A 6 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6772 (tt0) REVERT: A 38 ILE cc_start: 0.8209 (mm) cc_final: 0.7999 (mm) REVERT: A 49 MET cc_start: 0.7510 (tpt) cc_final: 0.7244 (tpt) REVERT: A 62 GLN cc_start: 0.7374 (mp10) cc_final: 0.6953 (mp10) REVERT: A 76 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.6887 (p90) REVERT: A 110 MET cc_start: 0.7513 (tpp) cc_final: 0.7287 (mmm) REVERT: A 150 LEU cc_start: 0.8246 (mp) cc_final: 0.8024 (mt) REVERT: A 154 ILE cc_start: 0.8080 (mt) cc_final: 0.7848 (mt) REVERT: A 181 HIS cc_start: 0.7366 (p-80) cc_final: 0.7153 (p-80) REVERT: A 233 SER cc_start: 0.8340 (p) cc_final: 0.7888 (m) REVERT: A 273 MET cc_start: 0.7436 (ttt) cc_final: 0.7190 (ttt) REVERT: B 50 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7579 (mpp-170) REVERT: B 114 LEU cc_start: 0.8012 (pp) cc_final: 0.7777 (mt) REVERT: B 167 ILE cc_start: 0.8334 (mt) cc_final: 0.8039 (mt) REVERT: B 216 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7668 (mtpt) REVERT: B 246 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7940 (ttmm) outliers start: 22 outliers final: 20 residues processed: 156 average time/residue: 0.2008 time to fit residues: 38.2195 Evaluate side-chains 168 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 58 TRP Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.0010 chunk 38 optimal weight: 0.5980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129577 restraints weight = 7676.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133668 restraints weight = 3781.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.136251 restraints weight = 2245.506| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4838 Z= 0.257 Angle : 0.729 7.913 6553 Z= 0.358 Chirality : 0.051 0.204 729 Planarity : 0.006 0.069 821 Dihedral : 6.776 74.506 640 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.46 % Allowed : 25.39 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.36), residues: 560 helix: -0.74 (0.32), residues: 261 sheet: -3.47 (0.90), residues: 25 loop : -2.13 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 58 HIS 0.006 0.001 HIS A 127 PHE 0.032 0.002 PHE B 119 TYR 0.018 0.001 TYR B 60 ARG 0.004 0.000 ARG A 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1508.54 seconds wall clock time: 27 minutes 50.89 seconds (1670.89 seconds total)